I have used the MG-Rast tools python code to download summary tables of sequence hits that fall into different Subsystems ontology categories. For instance, the following code summarizes 5 samples, compiles and downloads a table that is easily then read into other software:

mg-compare-functions.py \
  --ids "mgm4812503.3,mgm4812531.3,mgm4812526.3,mgm4812553.3,mgm4812451.3" \
  --level level3 \
  --source Subsystems \
  --format text \
  --evalue 10 > ~/Desktop/PhD/Metagenome/Download/mgRast_ontologyLVL3_list01.txt

I've removed my authentication token so this isn't exactly reproducible, but it makes a tab delimited text file that looks something like this:

mgm4812451.3    mgm4812503.3    mgm4812526.3    mgm4812531.3    mgm4812553.3
COG2363 25684   20011   29927   25736   15503
Carboxysome 6459    5200    7519    6074    4606
Respiratory_dehydrogenases_1    21806   19178   28776   21040   15472
Iron_acquisition_in_Vibrio  14557   14243   15804   12768   8607
Transport_of_Iron   7202    7436    8432    6641    5235

I'm trying to get a similar set of summary annotation tables for organisms from mg-Rast, but I can't find an analogous tool to the mg-compare-functions.py tool but for organisms. I have ~320 samples that I'd like to quickly compile into a table of summary hits by organism ID at roughly the genus level. How should I do this?

Thanks,
Dietrich